13,945 research outputs found
Persistent Homology Guided Force-Directed Graph Layouts
Graphs are commonly used to encode relationships among entities, yet their
abstractness makes them difficult to analyze. Node-link diagrams are popular
for drawing graphs, and force-directed layouts provide a flexible method for
node arrangements that use local relationships in an attempt to reveal the
global shape of the graph. However, clutter and overlap of unrelated structures
can lead to confusing graph visualizations. This paper leverages the persistent
homology features of an undirected graph as derived information for interactive
manipulation of force-directed layouts. We first discuss how to efficiently
extract 0-dimensional persistent homology features from both weighted and
unweighted undirected graphs. We then introduce the interactive persistence
barcode used to manipulate the force-directed graph layout. In particular, the
user adds and removes contracting and repulsing forces generated by the
persistent homology features, eventually selecting the set of persistent
homology features that most improve the layout. Finally, we demonstrate the
utility of our approach across a variety of synthetic and real datasets
Leveraging Citation Networks to Visualize Scholarly Influence Over Time
Assessing the influence of a scholar's work is an important task for funding
organizations, academic departments, and researchers. Common methods, such as
measures of citation counts, can ignore much of the nuance and
multidimensionality of scholarly influence. We present an approach for
generating dynamic visualizations of scholars' careers. This approach uses an
animated node-link diagram showing the citation network accumulated around the
researcher over the course of the career in concert with key indicators,
highlighting influence both within and across fields. We developed our design
in collaboration with one funding organization---the Pew Biomedical Scholars
program---but the methods are generalizable to visualizations of scholarly
influence. We applied the design method to the Microsoft Academic Graph, which
includes more than 120 million publications. We validate our abstractions
throughout the process through collaboration with the Pew Biomedical Scholars
program officers and summative evaluations with their scholars
Can Real Social Epistemic Networks Deliver the Wisdom of Crowds?
In this paper, we explain and showcase the promising methodology of testimonial network analysis and visualization for experimental epistemology, arguing that it can be used to gain insights and answer philosophical questions in social epistemology. Our use case is the epistemic community that discusses vaccine safety primarily in English on Twitter. In two studies, we show, using both statistical analysis and exploratory data visualization, that there is almost no neutral or ambivalent discussion of vaccine safety on Twitter. Roughly half the accounts engaging with this topic are pro-vaccine, while the other half are con-vaccine. We also show that these two camps rarely engage with one another, and that the con-vaccine camp has greater epistemic reach and receptivity than the pro-vaccine camp. In light of these findings, we question whether testimonial networks as they are currently constituted on popular fora such as Twitter are living up to their promise of delivering the wisdom of crowds. We conclude by pointing to directions for further research in digital social epistemology
Understanding Hidden Memories of Recurrent Neural Networks
Recurrent neural networks (RNNs) have been successfully applied to various
natural language processing (NLP) tasks and achieved better results than
conventional methods. However, the lack of understanding of the mechanisms
behind their effectiveness limits further improvements on their architectures.
In this paper, we present a visual analytics method for understanding and
comparing RNN models for NLP tasks. We propose a technique to explain the
function of individual hidden state units based on their expected response to
input texts. We then co-cluster hidden state units and words based on the
expected response and visualize co-clustering results as memory chips and word
clouds to provide more structured knowledge on RNNs' hidden states. We also
propose a glyph-based sequence visualization based on aggregate information to
analyze the behavior of an RNN's hidden state at the sentence-level. The
usability and effectiveness of our method are demonstrated through case studies
and reviews from domain experts.Comment: Published at IEEE Conference on Visual Analytics Science and
Technology (IEEE VAST 2017
Exploratory topic modeling with distributional semantics
As we continue to collect and store textual data in a multitude of domains,
we are regularly confronted with material whose largely unknown thematic
structure we want to uncover. With unsupervised, exploratory analysis, no prior
knowledge about the content is required and highly open-ended tasks can be
supported. In the past few years, probabilistic topic modeling has emerged as a
popular approach to this problem. Nevertheless, the representation of the
latent topics as aggregations of semi-coherent terms limits their
interpretability and level of detail.
This paper presents an alternative approach to topic modeling that maps
topics as a network for exploration, based on distributional semantics using
learned word vectors. From the granular level of terms and their semantic
similarity relations global topic structures emerge as clustered regions and
gradients of concepts. Moreover, the paper discusses the visual interactive
representation of the topic map, which plays an important role in supporting
its exploration.Comment: Conference: The Fourteenth International Symposium on Intelligent
Data Analysis (IDA 2015
A signaling visualization toolkit to support rational design of combination therapies and biomarker discovery: SiViT
Targeted cancer therapy aims to disrupt aberrant cellular signalling pathways. Biomarkers are surrogates of pathway state, but there is limited success in translating candidate biomarkers to clinical practice due to the intrinsic complexity of pathway networks. Systems biology approaches afford better understanding of complex, dynamical interactions in signalling pathways targeted by anticancer drugs. However, adoption of dynamical modelling by clinicians and biologists is impeded by model inaccessibility. Drawing on computer games technology, we present a novel visualisation toolkit, SiViT, that converts systems biology models of cancer cell signalling into interactive simulations that can be used without specialist computational expertise. SiViT allows clinicians and biologists to directly introduce for example loss of function mutations and specific inhibitors. SiViT animates the effects of these introductions on pathway dynamics, suggesting further experiments and assessing candidate biomarker effectiveness. In a systems biology model of Her2 signalling we experimentally validated predictions using SiViT, revealing the dynamics of biomarkers of drug resistance and highlighting the role of pathway crosstalk. No model is ever complete: the iteration of real data and simulation facilitates continued evolution of more accurate, useful models. SiViT will make accessible libraries of models to support preclinical research, combinatorial strategy design and biomarker discovery
Complex Systems Science: Dreams of Universality, Reality of Interdisciplinarity
Using a large database (~ 215 000 records) of relevant articles, we
empirically study the "complex systems" field and its claims to find universal
principles applying to systems in general. The study of references shared by
the papers allows us to obtain a global point of view on the structure of this
highly interdisciplinary field. We show that its overall coherence does not
arise from a universal theory but instead from computational techniques and
fruitful adaptations of the idea of self-organization to specific systems. We
also find that communication between different disciplines goes through
specific "trading zones", ie sub-communities that create an interface around
specific tools (a DNA microchip) or concepts (a network).Comment: Journal of the American Society for Information Science and
Technology (2012) 10.1002/asi.2264
SPECTRUM-BASED AND COLLABORATIVE NETWORK TOPOLOGY ANALYSIS AND VISUALIZATION
Networks are of significant importance in many application domains, such as World Wide Web and social networks, which often embed rich topological information. Since network topology captures the organization of network nodes and links, studying net- work topology is very important to network analysis. In this dissertation, we study networks by analyzing their topology structure to explore community structure, the relationship among network members and links as well as their importance to the belonged communities. We provide new network visualization methods by studying network topology through two aspects: spectrum-based and collaborative visualiza- tion techniques.
For the spectrum-based network visualization, we use eigenvalues and eigenvectors to express network topological features instead of using network datasets directly. We provide a visual analytics approach to analyze unsigned networks based on re- cent achievements on spectrum-based analysis techniques which utilize the features of node distribution and coordinates in the high dimensional spectral space. To assist the interactive exploration of network topologies, we have designed network visual- ization and interactive analysis methods allowing users to explore the global topology structure.
Further, to address the question of real-life applications involving of both positive and negative relationships, we present a spectral analysis framework to study both signed and unsigned networks. Our framework concentrates on two problems of net-
work analysis - what are the important spectral patterns and how to use them to study signed networks. Based on the framework, we present visual analysis methods, which guide the selection of k-dimensional spectral space and interactive exploration of network topology.
With the increasing complexity and volume of dynamic networks, it is important to adopt strategies of joint decision-making through developing collaborative visualiza- tion approaches. Thus, we design and develop a collaborative detection mechanism with matrix visualization for complex intrusion detection applications. We establish a set of collaboration guidelines for team coordination with distributed visualization tools. We apply them to generate a prototype system with interactions that facilitates collaborative visual analysis.
In order to evaluate the collaborative detection mechanism, a formal user study is presented. The user study monitored participants to collaborate under co-located and distributed collaboration environments to tackle the problems of intrusion detection. We have observed participants’ behaviors and collected their performances from the aspects of coordination and communication. Based on the results, we conclude several coordination strategies and summarize the values of communication for collaborative visualization.
Our visualization methods have been demonstrated to be efficient topology explo- ration with both synthetic and real-life datasets in spectrum-based and collaborative exploration. We believe that our methods can provide useful information for future design and development of network topology visualization system
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